rs900238

Positions:

• chr8-48683498-C-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NR_105002.1(LOC101929268):​n.357-11926C>T variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.647 in 152,056 control chromosomes in the GnomAD database, including 36,091 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.65 (36091 hom., cov: 32)
• Consequence: LOC101929268 NR_105002.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0370

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.821 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC101929268	NR_105002.1	n.357-11926C>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
	ENST00000522575.1	n.357-11926C>T		intron_variant, non_coding_transcript_variant		2
	ENST00000654201.1	n.58-11253C>T		intron_variant, non_coding_transcript_variant
	ENST00000657307.1	n.25-11926C>T		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.647 AC: 98361 AN: 151938 Hom.: 36094 Cov.: 32

Gnomad AFR AF: 0.278

Gnomad AMI AF: 0.775

Gnomad AMR AF: 0.658

Gnomad ASJ AF: 0.687

Gnomad EAS AF: 0.715

Gnomad SAS AF: 0.637

Gnomad FIN AF: 0.868

Gnomad MID AF: 0.699

Gnomad NFE AF: 0.827

Gnomad OTH AF: 0.656

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.647 AC: 98382 AN: 152056 Hom.: 36091 Cov.: 32 AF XY: 0.651 AC XY: 48377 AN XY: 74338

Gnomad4 AFR AF: 0.278

Gnomad4 AMR AF: 0.657

Gnomad4 ASJ AF: 0.687

Gnomad4 EAS AF: 0.716

Gnomad4 SAS AF: 0.637

Gnomad4 FIN AF: 0.868

Gnomad4 NFE AF: 0.827

Gnomad4 OTH AF: 0.656

Alfa AF: 0.757 Hom.: 21872

Bravo AF: 0.617

Asia WGS AF: 0.637 AC: 2213 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	1.3
DANN	Benign	0.27

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs900238; hg19: chr8-49596058;